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Applied and Environmental Microbiology, December 2005, p. 7941-7947, Vol. 71, No. 12
0099-2240/05/$08.00+0 doi:10.1128/AEM.71.12.7941-7947.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Danish Institute for Food and Veterinary Research, 1790 Copenhagen V, Denmark,1 Statens Serum Institute, 2300 Copenhagen S, Denmark2
Received 2 March 2005/ Accepted 24 August 2005
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Class I integrons (in-1) contribute to the spread of antimicrobial resistance genes and have been found in Enterobacteriaceae and other gram-negative bacteria (7), but they have also been found in a few gram-positive bacteria. Martin et al. were the first to report integrons in gram-positive bacteria; these authors found transposon-borne integrons in Mycobacterium fortuitum (18). An int-1-like gene truncated by the insertion sequence IS6100 located on the 27.8-kb plasmid pTET3, which also carries a newer Tcr gene, tet (32), has been found in Corynebacterium glutamicum (31). Clark et al. found integrons with aadA1 gene cassettes on an 80-kb transferable plasmid in Enterococcus faecalis (5). Recently, Nandi et al. found that gram-positive bacteria present in poultry litter were a major reservoir for in-1, especially among Corynebacterium spp. (20).
Tcr genes have not been found as gene cassettes in class I integrons, but have been found associated with class I integrons on self-transferable plasmids in both gram-positive and gram-negative bacteria such as Salmonella, Aeromonas, and Corynebacterium spp. (10, 11, 16, 31).
We investigated the presence of commonly found Tcr genes and class I integrons in bacteria isolated from manured soil and pigsty environment. Our purpose was to investigate whether environmental bacteria constitute a reservoir that could contribute to the spread of antimicrobial resistance between the animal and human populations.
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Farm 1 kept animal waste as a dunghill, and this manure was spread on fields once a year in April. Farm 2 also kept animal waste as a dunghill, and manure was spread once a year in August. The capacity of farm 1 and 2 was 700 and 1,800 pigs/year, respectively. Pig manure on farms 3, 4, A, B, and C was kept in large slurry containers. This manure slurry was spread in the fields of the respective farms once a year around May. The capacities of these five farms were 2,200, 900, 1,350, 1,100, and 1,250 pigs per year, respectively. Use of tetracyclines, aminoglycosides, and sulfonamides/trimethoprim has been documented for farms A, B, and C. None of the three farms used aminoglycosides. Farms A, B, and C used 285, 345, and 6,229 g of tetracycline/year and 96, 169, and 1,136 g of sulfadiazin and trimethoprim (5:1)/year, respectively.
Bacterial isolates from farms and fields.
Soil samples were collected on the eight farms as previously described (15, 29). Ten to twenty-five soil samples were collected from each farm, and bacterial isolates were recovered from the soil as previously described (29).
Bacteria from pigsty environments were isolated from fecal samples collected on three Danish pig farms (12 samples on farm 2 and 1 sample each on farms A and C). Approximately 100 g of samples were collected 1 m apart. Two grams of samples were added to 20 ml of 0.9% saline and shaken on a water bath at 120 rpm and 25°C for 1 h. The samples were serially 10-fold diluted in 0.9% saline and plated by surface spreading onto Luria-Bertani (LB) agar (25) and MacConkey agar (Oxoid, Greve, Denmark), both supplemented with tetracycline (8 µg/ml; Sigma-Aldrich, Brøndby, Denmark). The Escherichia coli isolates were isolated from the MacConkey plates and identified by using API 20E (bioMérieux, Marcy l'Etoile, France) and serotyped (32). The other pigsty isolates were isolated on LB agar plates.
From each soil or fecal sample one to three isolates were included in this investigation; none of the isolates from the same sample were from the same genus.
All isolates (except E. coli) were Gram stained and tested for oxidase, catalase, mobility, and for their oxidative or fermentative activity. The in-1-positive bacteria were identified by 16S rRNA sequencing by using primers 16S 10FX and 16S 519R (Table 1) from positions 13 to 545 (GenBank accession no. X80745). DNA sequencing was performed as described below. The obtained sequences were compared by use of the BLAST program (version 2.2.9) with sequences submitted to GenBank. The identification of Pseudomonas and Alcaligenes spp. was verified by use of API20NE and for Enterobacter sp. by use of API 20E (bioMérieux).
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TABLE 1. Bacterial strains and class 1 integron-positive isolates used in this study
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32 µg/ml. Since not all of the species have standardized and well-characterized breakpoints, approximations were used in the present investigations. The measured MICs for the resistant isolates were higher by a factor of four or more over the used breakpoints for all antimicrobials, except in some cases involving streptomycin and spectinomycin, in which the term "reduced in susceptibility" was used.
PCR detection of in-1 and Tcr genes.
The primers used in the present study are listed in Table 2. Tcr gram-negative (n = 164) and gram-positive (n = 49) soil isolates and gram-negative (n = 21) and gram-positive (n = 23) pigsty isolates were screened for in-1 by use of three primer sets: qacE
1-F and qacE
1-B, qacE
1-F and Sul-1B, and Att1-F and 3'CS-B (Table 2). Sixty of the gram-negative soil isolates (including the in-1-positive isolates, resulting in six to eight isolates from each farm) and all of the gram-negative pigsty isolates (20) were also screened for the Tcr genes tet(A), tet(B), and tet(C). All gram-negative in-1-positive isolates that did not contain tet(A-C) (n = 3) were screened for tet(D), tet(E), tet(G), tet(31), and tet(34). Six Arthrobacter isolates were screened for tet(M), tet(O), tet(S), tet(L), tet(K), tet(Z), and tet(33). Since tet(33) was found in all six isolates and none of the other tet genes were found, the remaining gram-positive isolates (n = 66) were screened for tet(33). Transconjugants were screened for in-1 and the same tet genes that the respective donors contained.
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TABLE 2. Primers used in this study for detection of Tcr genes, class 1 integrons, and 16S RNA by PCR and DNA sequencing
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Mating experiments with in-1-positive soil isolates.
Bacteria from the soil environment, intestinal system, and a pathogen were chosen as recipients. Mating experiments with gram-negative donors were done with E. coli [1005(R)] and Pseudomonas putida [KT2442(N)] as recipients. For gram-positive matings, E. faecalis (JH2-2) was used as the recipient. Three Arthrobacter isolates (R343, R344, and R345) were also used as donors to the recipients: E. coli [1005(R)], P. putida [KT2442(N)], E. faecium (BM4105), and Staphylococcus aureus (8794RF) (Table 1) as described by Hammerum et al. (12). Exponentially growing donor and recipient cultures were washed twice in 0.9% saline and mixed 1:1 at an optical density at 450 nm of 0.5. A volume of 500 µl of donor-recipient mixture was added to a filter placed on an LB agar plate for the gram-negative recipients and on a calf blood agar plate for the gram-positive recipients. The agar plate with the mixed cell suspension was incubated at 25°C for 20 to 24 h. The cells were serially diluted, and appropriate dilutions were plated onto selective media in order to determine the extent of horizontal transfer. Transconjugants of E. coli and P. putida were selected on LB agar supplemented with 8 µg of tetracycline and 100 µg of rifampin (Sigma-Aldrich, Brøndby, Denmark)/ml. Transconjugants for E. faecalis, E. faecium, and S. aureus were selected on brain heart infusion agar (Difco, Detroit, MI) supplemented with 8 µg of tetracycline, 25 µg of rifampin, and 25 µg of fusidic acid (Sigma-Aldrich)/ml. The transconjugants were restreaked on selective plates.
Plasmid isolation and Southern blotting.
All donors and gram-negative transconjugants with a transferable integron and Tcr were screened for plasmids by use of an alkaline lysis method (9), followed by gel electrophoresis on a 0.8% Tris-borate-EDTA gel at 80 V for 5 h. Southern blots on undigested and BamHI-digested plasmids were performed. The blots were hybridized with two digoxigenin-labeled DNA probes for the presence of the 3' segment of class 1 integrons using the PCR product (225 bp) amplified by the primers qacE
1-F and qacE
1-B and for tet(A) (956 bp) by using the PCR products amplified by tet(A)-1 and tet(A)-2, respectively (Table 2).
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Class 1 integrons were found in 5% (8 of 164) of the gram-negative soil isolates, 33% (7 of 21) of the gram-negative pigsty isolates, 12% (6 of 49) of the gram-positive soil isolates, and 17% (4 of 23) of the gram-positive pigsty isolates. The soil isolates belonged to species of Pseudomonas, Alcaligenes, Corynebacterium, and Arthrobacter The pigsty isolates were identified as E. coli, Enterobacter spp., Arthrobacter spp., and one unidentified gram-positive species with 96% homology to 16S RNA of Leucobacter komagatae (GenBank accession no. AJ746337, positions 10 to 750) (Table 1).
Sixty of the Tcr soil isolates, including the in-1-positive isolates and all 21 gram-negative pigsty isolates, were screened for tet(A), tet(B), and tet(C). tet(A) was found in three Alcaligenes spp. from soil, seven E. coli strains, and one Enterobacter sp. from a pigsty, tet(B) was found in one E. coli pigsty isolate, and tet(C) was found in two Pseudomonas spp. from soil. The remaining 67 gram-negative isolates did not contain any of the three tet genes [tet(A), tet(B) or tet(C)]. All tet(A) or tet(C) genes were found among in-1-positive isolates except one tet(A)-positive E. coli. Three in-1-positive soil isolates did not contain tet(A-C) or any of the other tet genes for which we screened.
Ten isolates were positive for tet(33), and all isolates had, in addition, in-1 (Table 1). The PCR product of tet(33) was sequenced in seven isolates (R70, R344, R345 [GenBank accession no. DQ077487], R1809, R1811, R1554, and R2139) and had 99 to 100% homology to tet(33) from C. glutamicum (GenBank accession no. AJ420072, positions 23085 to 23840). The remaining 62 gram-positive isolates did not contain tet(33).
None of the soil isolates from farms A, 1, and 5 (field not treated with animal manure) contained in-1 or any of the tet genes for which we tested.
Mating experiments and plasmids.
Eleven integron-positive Tcr soil isolates were used as donors in mating experiments with the recipients E. coli and P. putida. The two A. faecalis isolates showed cotransfer of tet(A) and in-1 to both P. putida and E. coli. A Pseudomonas sp. showed cotransfer of tet(C) and in-1 to P. putida. One Pseudomonas sp. with unidentified Tcr showed cotransfer of Tcr and in-1 to E. coli (Table 3). None of the A. protophormiae isolates showed transfer to any of the recipients chosen in the mating experiments.
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TABLE 3. Filter-mating experiments with gram-negative donors and E. coli and P. putida recipients
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FIG. 1. Southern blot of plasmid extractions. (A) Hybridized with class 1 integron probe (qacE 1). Lane 1, HindIII-cut marker; lane 2, A. faecalis R194; lane 3, transconjugant R194-P; lane 4, transconjugant R194-E; lane 5, A. faecalis R214; lane 6, transconjugant R214-P; lane 7, transconjugant R214-E; lane 8, recipient P. putida; lane 9, recipient E. coli. (B) Hybridized with Tcr tet(A) probe. Lane 1, HindIII-cut marker; lane 2, A. faecalis R194; lane 3, transconjugant R194-P; lane 4, transconjugant R194-E; lane 5, A. faecalis R214; lane 6, transconjugant R214-P; lane 7, transconjugant R214-E; lane 8, recipient P. putida; lane 9, recipient E. coli. (C) BamHI-restricted 36-kb plasmids hybridized with tet(A). Lane 1, strain R194; lane 2, transconjugant R194-P; lane 3, transconjugant R194-E; lane 4, recipient P. putida; lane 5, E. coli; lane 6, strain R214; lane 7, transconjugant R214-P; lane 8, transconjugant R214-E; lane 9, HindIII-digested marker. The size markers were based on HindIII-digested marker and plasmids extracted from E. coli R39.
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All in-1-positive isolates, recipients, and transconjugants were tested for antimicrobial resistance and showed resistance to three to nine drugs (Table 1). All in-1-positive isolates were resistant to tetracycline, streptomycin, spectinomycin (except one pseudomonad), and sulfonamethoxazole. The E. coli isolates were in addition resistant to ampicillin and trimethoprim. Of the pseudomonads, one was resistant to nine antimicrobial agents, and the Alcaligenes isolates were resistant to six or seven drugs (Table 1).
Transconjugants from mating experiments differed from the respective recipients in being resistant to tetracycline and sulfonamethoxazole and resistant or reduced in susceptibility to streptomycin and spectinomycin. P. putida transconjugants R347-P, R194-P and R214-P were also resistant to trimethoprim like their respective donors (Table 1).
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Pseudomonas isolates showed cotransfer of Tcr and in-1 to either P. putida or E. coli. One Pseudomonas isolate contained tet(C), and one isolate did not contain any of the tet genes for which it was screened but might contain a new class of tet genes.
Horizontal cotransfer of tet(A) and in-1 have been observed among Aeromonas species from freshwater (16, 27). This demonstrates once more how a common gene pool can be shared between organisms belonging to different environments.
Thus far, no published studies have described Tcr genes or integrons in the genus Arthrobacter probably because of a limited focus of antimicrobial resistance in these bacteria. The six Arthrobacter spp. in the present study all contained the Tcr gene tet(33), which was previously described for C. glutamicum (31). In earlier studies, integrons were found in gram-positive isolates of C. glutamicum, whose genus is closely related to Arthrobacter (22). gram-positive bacteria, especially Corynebacterium spp., were found to be a reservoir for in-1 in poultry litter (20). Coryneform bacteria such as Arthrobacter and Corynebacterium spp. seem to be important reservoirs for in-1 and not only Enterobacteriaceae and other gram-negative bacteria (20).
Even though no element containing in-1 and tet(33) was found to exist in the gram-positive strains, a very clear pattern existed among the gram-positive bacteria since all in-1-positive isolates also contained tet(33). It is therefore likely that these bacteria contain in-1 and tet(33) on the same genetic element and may be related to the pTET3 from C. glutamicum (31). The bacteria were isolated from two different pigsties and three farmland soils and belonged to four species: A. nicotianae, A. protophormiae, C. glutamicum, and an unidentified gram-positive bacterium. The presence of tet(33) in different soil bacteria indicates the gene to be horizontally spread in the soil environment rather than clonally spread, although none of the Arthrobacter isolates or other gram-positive bacteria could cotransfer integron and Tcr to any of the gram-negative or gram-positive recipients. Intergenic transfer of Inc plasmids between E. coli and Arthrobacter has been observed before (17), so the lack of transfer of Tcr in the present study may have been due to the choice of recipients.
The presence of Arthrobacter or other indigenous soil bacteria with multiple resistances within a pigsty environment may lead to the transfer of resistance genes from soil bacteria to bacteria of animal origin. Alcaligenes, Pseudomonas, and Arthrobacter spp. are very common bacteria in soil and water and are therefore likely to be in close contact with humans and animals via crops and drinking water. The fact that these bacteria are soil bacteria means that they can survive and grow in the environment for a long period of time. Arthrobacter species are now recognized as opportunistic pathogens (8, 14). Arthrobacter may therefore be an important reservoir for both in-1 and Tcr genes.
The presence of aadA gene cassettes in all in-1 resulted in resistance to streptomycin and/or spectinomycin, in addition to sulfonamide and tetracycline resistance in these isolates (Table 1). This indicates that soil bacteria can contribute to the spread of multidrug resistance. One Pseudomonas and three Alcaligenes isolates from soil contained a variant of aadA11 from a clinical isolate of E. coli, recently submitted to GenBank (accession no. AJ567827). This gene cassette may be more frequently present in the soil environment than in the human reservoir and could have been exchanged between the different reservoirs.
Whether the soil environment acts as a reservoir for multidrug resistance (encoded by in-1 and tetracycline resistance genes) or whether these genes are present in the soil environment as a result of spreading animal manure to the farmland soil was not determined here, but it is interesting that none of the isolates from the soil not treated with animal manure (farm 5) contained in-1 or tet genes. The results may indicate that multidrug resistance caused by tet genes and in-1 can be transferred from the soil environment to animals and humans via crops or drinking water.
Our overall conclusion is that soil bacteria in close contact with manure or pigsty environments seem to have an important role in horizontal spread of multidrug resistance (especially plasmid-mediated resistance encoded by class 1 integron gene cassettes and tet genes). The increased use of tetracyclines in food animal production may contribute to increased multidrug resistance in bacteria.
GenBank submissions.
The sequence of the gene cassettes (aadA11, dfrA1) from A. faecalis R194 and tet(33) Arthrobacter protophorniae described in the present study have been submitted to GenBank (GenBank submission no. DQ074759 and DQ077487, respectively).
We thank Lise Christensen, Christina Aaby Svendsen, Christina Alhblad, and Anette Nielsen for excellent technical assistance and René Sjøgren Hendriksen for useful discussions. We thank Satoru Suzuki for providing a tet(34)-positive strain, Henning Sørum for a tet(31)-positive strain, and Andreas Tauch for tet(Z) and tet(33) probes.
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